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Search for clues in the flounder genome

06.02.2014

What does the Chinese flounder have in common with a bird?

They have both developed the same mechanism for determining sex over the course of evolution, and have done so completely independently of one another. This is the recent discovery made by an international team of scientists with Würzburg involvement.

The sex of any mammal – humans included – and of a number of other living beings is usually decided by a very specific combination of chromosomes: XX for female; XY for male. However, nature boasts many different ways of determining sex. In birds, most snakes, some fish, and even butterflies, for example, we find the so-called ZW/ZZ system. In this case, the females carry one W and one Z chromosome in their cells, while the males have two Z chromosomes. This is also true for the Chinese flounder Cynoglossus semilaevis – a popular edible fish from Asia, which is bred in aquaculture there and can grow up to 40 centimeters long.

An international team of scientists has now succeeded in completely decoding the genome of this species of flounder. For the first time ever they have also been able to fully sequence a W chromosome and trace its emergence over the course of evolution. Würzburg biochemist and geneticist Professor Manfred Schartl played an instrumental role in the project. Schartl is Chairman of the Department of Physiological Chemistry at the University’s Biocenter. The scientific journal Nature Genetics has now published the results of this work.

“Our work shows that in the Chinese flounder and in birds alike the same ancient chromosomes have developed into sex chromosomes over the course of evolution – the sex chromosomes have the same ancestors in both cases. And this process took place entirely independently and at different times,” is how Schartl summarizes the main finding of this work. Surprisingly, even the gene that is largely responsible for sex determination in birds – dmrt1 – has gone through a development process in the flounder that is similar to that in birds.

Sex chromosomes pose problems

When scientists try to sequence sex chromosomes, they are faced with a mountain of problems: “For one thing, these chromosomes have undergone a major degeneration process over the course of evolution. For another, they have DNA segments that are repeated extensively,” says Manfred Schartl. This makes the search for individual genes and their organization so labor-intensive and is probably also the reason why only a tiny number of Y chromosomes have so far been fully sequenced – including those in humans and chimpanzees. Even less was previously known about the genetic information of W chromosomes. For the work that has now been published researchers have fully sequenced a W chromosome for the first time ever.

There are two main reasons why the team focused in their study on a flounder: “Measured in geological time, fish are one of the living creatures that only relatively recently developed sex chromosomes,” explains Schartl. Unlike in birds, for which this point in time was some 200 million years ago, the chromosomes in fish have therefore had comparatively little time to degenerate. In addition, flounder have a comparatively small genome.

The genome of the flounder

21,516 protein-coding genes were counted by the scientists in the genome of the Chinese flounder – humans have some 20,000 to 25,000 according to the National Genome Research Network (NGFN). Roughly 197 million years ago, the flounder line developed from that of bony fish. It was not until much later, only about 30 million years ago, that the sex chromosomes of the flounder developed – long after the phylogenetic trees of mammals, birds, and fish had separated.

Around 1,000 genes are carried by the Z chromosome of flounder, while there are 317 on the W chromosome. This is much more than in birds, which possess 26 genes on the W chromosome. And also far more than in humans and chimpanzees, on whose Y chromosomes 40 to 80 intact genes can be found. “This observation suggests that the evolutionary origin of the sex chromosomes in flounder was comparatively recent,” says Schartl. Simply put, the W chromosome in flounder has not had enough time yet to degenerate in a similar fashion to the chromosomes of birds and mammals – after all, these have had several hundred million years in which to do so.

What determines sex

What ultimately determines sex? A gene on the Z chromosome that is responsible for male attributes? Or a gene on the W chromosome that turns its male carrier into a female one? Or a combination of the two? For birds, this question remains unanswered, so the research team has tried to find an answer by looking at the Chinese flounder. “The flounder lends itself to this study because it is possible with flounder to alter sexual development by exposing the offspring to higher temperatures,” says Schartl. At an ambient temperature of 22 degrees at the time of the corresponding period of development 14 percent of flounder offspring spontaneously change sex, whereas at 28 degrees this rate increases to up to 73 percent. So-called pseudo-males then develop instead of females.

In their study, the scientists crossed these pseudo-males with normal females and let the offspring grow at normal temperatures. The surprising result was a clear surplus of males. As expected, all the ZZ carriers were male, but what was not expected, however, was that 94 percent of the ZW carriers also developed into pseudo-males. “These experiments show that sex determination in flounder is controlled by a mechanism on the Z chromosome which initiates a male development,” is how Schartl explains the findings. Nevertheless, the scientists cannot rule out with absolute certainty the possibility that there is also a second mechanism, controlled by genes that also lie on the Z chromosome, which starts at high temperatures.

A chromosome is disappearing

Is the Y chromosome in humans at risk of extinction? This question has been and will continue to be addressed in science from time to time. After all, it has already lost much of its genetic information over the course of evolution. However, as researchers showed recently, this loss has slowed markedly over the past 25 million years. This suggests that the loss must have happened much earlier.

The W chromosome of the Chinese flounder has existed for around 30 million years. During this time it has lost about two thirds of its original genetic information. If this process continues at the same rate, it will take a mere ten million years for the W chromosome to reach the same state as the Y chromosome in humans currently.

From the scientists’ standpoint, this observation shows that the loss of genetic material on sex chromosomes must be an early and rapid phenomenon in their development.

“Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle”. Nature Genetics, published online on February 2, 2014. DOI: 10.1038/ng.2890

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